[ Started: 2024-10-17 12:22:58 CEST ]
[ OmnipathR v3.13.28 for BioC-3.20 from https://github.com/saezlab/OmnipathR@master (4007299 2024-10-16 12:16:56) ]

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘OmnipathR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 12:23:11] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 12:23:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmp4WS0BM/Rinst1c7319336c7678/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmp4WS0BM/Rinst1c7319336c7678/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmp4WS0BM/Rinst1c7319336c7678/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmp4WS0BM/Rinst1c7319336c7678/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2024-10-17 12:23:11] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 12:23:11] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 12:23:11] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-10-17 12:23:11] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] HTTP 200
[2024-10-17 12:23:11] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 12:23:11] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.

Quitting from lines 216-218 [network] (bioc_workshop.Rmd)
Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- failed re-building ‘bioc_workshop.Rmd’

--- re-building ‘cosmos.Rmd’ using rmarkdown
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-10-17 12:23:11] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-10-17 12:23:11] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-10-17 12:23:11] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html

Quitting from lines 176-179 [omnipath] (cosmos.Rmd)
Error: processing vignette 'cosmos.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- failed re-building ‘cosmos.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2024-10-17 12:23:12] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2024-10-17 12:23:12] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2024-10-17 12:23:12] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-10-17 12:23:12] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-10-17 12:23:12] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html

Quitting from lines 67-69 [get] (db_manager.Rmd)
Error: processing vignette 'db_manager.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- failed re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2024-10-17 12:23:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2024-10-17 12:23:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2024-10-17 12:23:12] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-10-17 12:23:12] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-10-17 12:23:12] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html

Quitting from lines 46-51 [unnamed-chunk-2] (drug_targets.Rmd)
Error: processing vignette 'drug_targets.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- failed re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2024-10-17 12:23:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2024-10-17 12:23:12] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-10-17 12:23:12] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-10-17 12:23:12] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html

Quitting from lines 56-58 [load-interactions] (extra_attrs.Rmd)
Error: processing vignette 'extra_attrs.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- failed re-building ‘extra_attrs.Rmd’

--- re-building ‘nichenet.Rmd’ using rmarkdown
--- finished re-building ‘nichenet.Rmd’

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2024-10-17 12:23:13] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-17 12:23:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 12:23:14] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2024-10-17 12:23:14] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2024-10-17 12:23:14] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-10-17 12:23:14] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-10-17 12:23:14] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html

Quitting from lines 167-175 [interactions] (omnipath_intro.Rmd)
Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- failed re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2024-10-17 12:23:14] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2024-10-17 12:23:14] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-10-17 12:23:14] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-10-17 12:23:14] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html

Quitting from lines 56-67 [tfcensus-op] (paths.Rmd)
Error: processing vignette 'paths.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- failed re-building ‘paths.Rmd’

SUMMARY: processing the following files failed:
  ‘bioc_workshop.Rmd’ ‘cosmos.Rmd’ ‘db_manager.Rmd’ ‘drug_targets.Rmd’ ‘extra_attrs.Rmd’
  ‘omnipath_intro.Rmd’ ‘paths.Rmd’

Error: Vignette re-building failed.
Execution halted
[ Finished: 2024-10-17 12:23:14 CEST ]